Impact of compounding error on strategies for subtyping pathogenic bacteria

Douglas R Call; Lisa Orfe; Margaret A Davis; Stacey Lafrentz; Min-Su Kang

doi:10.1089/fpd.2008.0097

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Impact of compounding error on strategies for subtyping pathogenic bacteria

Journal article

Open access

Peer reviewed

Impact of compounding error on strategies for subtyping pathogenic bacteria

Douglas R Call, Lisa Orfe, Margaret A Davis, Stacey Lafrentz and Min-Su Kang

Foodborne pathogens and disease, Vol.5(4), pp.505-516

08/2008

DOI: https://doi.org/10.1089/fpd.2008.0097

Handle:

https://hdl.handle.net/2376/110616

PMCID: PMC3186708

PMID: 18713065

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Abstract

Nucleic Acid Hybridization - methods

DNA Probes

Genes, Bacterial

Species Specificity

Vibrio parahaemolyticus - classification

Salmonella enterica - genetics

Genetic Markers

Bacterial Typing Techniques - methods

Minisatellite Repeats

Microspheres

Vibrio parahaemolyticus - genetics

DNA, Bacterial - genetics

Electrophoresis, Gel, Pulsed-Field - methods

Sensitivity and Specificity

Alleles

Listeria monocytogenes - classification

Polymerase Chain Reaction

Listeria monocytogenes - genetics

Salmonella enterica - classification

Comparative-omics will identify a multitude of markers that can be used for intraspecific discrimination between strains of bacteria. It seems intuitive that with this plethora of markers we can construct higher resolution subtyping assays using discrete markers to define strain "barcodes." Unfortunately, with each new marker added to an assay, overall assay robustness declines because errors are compounded exponentially. For example, the difference in accuracy of strain classification for an assay with 60 markers will change from 99.9% to 54.7% when average probe accuracy declines from 99.999% to 99.0%. To illustrate this effect empirically, we constructed a 19 probe bead-array for subtyping Listeria monocytogenes and showed that despite seemingly reliable individual probe accuracy (>97%), our best classification results at the strain level were <75%. A more robust strategy would use as few markers as possible to achieve strain discrimination. Consequently, we developed two variable number of tandem repeat (VNTR) assays (Vibrio parahaemolyticus and L. monocytogenes) and demonstrate that these assays along with a published assay (Salmonella enterica) produce robust results when products were machine scored. The discriminatory ability with four to seven VNTR loci was comparable to pulsed-field gel electrophoresis. Passage experiments showed some instability with ca. 5% of passaged lines showing evidence for new alleles within 30 days (V. parahaemolyticus and S. enterica). Changes were limited to a single locus and allele so conservative rules can be used to determine strain matching. Most importantly, VNTRs appear robust and portable and can clearly discriminate between strains with relatively few loci thereby limiting effects of compounding error.

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Title: Impact of compounding error on strategies for subtyping pathogenic bacteria
Creators: Douglas R Call - Department of Veterinary Microbiology and Pathology, Washington State University, Pullman, Washington 99164-7040, USA. drcall@wsu.edu
Lisa Orfe
Margaret A Davis
Stacey Lafrentz
Min-Su Kang
Publication Details: Foodborne pathogens and disease, Vol.5(4), pp.505-516
Academic Unit: Paul G. Allen School for Global Animal Health
Publisher: United States
Grant note: N01-AI-30055 / NIAID NIH HHS
Identifiers: 99900547492801842
Language: English
Resource Type: Journal article